With a little practice, it can easily become a medium for your own thinking process. One of the best features of Freemind is that you can define your own key-mappings, which makes it more productive than other mind-mapping (brain-storming) tools out there. Also, though it is a mature software, it is still actively developed; so you can expect more features coming in as time goes by.

I like to use Tomboy for note-taking and for brainstorming. It works really well, and you can organize all your thoughts into different "notebooks" to keep everything together. IT works with wikiwords, so you can type a word LikeThis and it will automatically link to the note called LikeThis. If there's no note by that name, Tomboy will create it.